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- EMDB-20081: CryoEM structure of Arabidopsis DDR' complex (DRD1 peptide-DMS3-RDM1) -

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Basic information

Entry
Database: EMDB / ID: EMD-20081
TitleCryoEM structure of Arabidopsis DDR' complex (DRD1 peptide-DMS3-RDM1)
Map data
Sample
  • Complex: DDR' complex of DRD1 peptide with DMS3 and RDM1
    • Protein or peptide: Protein RDM1
    • Protein or peptide: Protein DEFECTIVE IN MERISTEM SILENCING 3
    • Protein or peptide: Protein CHROMATIN REMODELING 35
KeywordsSMC-hinge / Coiled-coil / SNF2 / RNA-directed DNA methylation / PLANT PROTEIN
Function / homology
Function and homology information


RNA polymerase IV transcription regulator complex / RNA polymerase V complex / gene silencing by siRNA-directed DNA methylation / heterochromatin organization / negative regulation of DNA methylation-dependent heterochromatin formation / siRNA processing / regulatory ncRNA-mediated gene silencing / positive regulation of chromatin binding / DNA methylation-dependent constitutive heterochromatin formation / ATP-dependent chromatin remodeler activity ...RNA polymerase IV transcription regulator complex / RNA polymerase V complex / gene silencing by siRNA-directed DNA methylation / heterochromatin organization / negative regulation of DNA methylation-dependent heterochromatin formation / siRNA processing / regulatory ncRNA-mediated gene silencing / positive regulation of chromatin binding / DNA methylation-dependent constitutive heterochromatin formation / ATP-dependent chromatin remodeler activity / cellular response to exogenous dsRNA / defense response to fungus / pericentric heterochromatin / helicase activity / hydrolase activity / protein homodimerization activity / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
SNF2 domain-containing protein CLSY/DRD1 / Protein RDM1, plant / RDM1 superfamily / RNA-directed DNA methylation 1 / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain ...SNF2 domain-containing protein CLSY/DRD1 / Protein RDM1, plant / RDM1 superfamily / RNA-directed DNA methylation 1 / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protein DEFECTIVE IN MERISTEM SILENCING 3 / Protein RDM1 / Protein CHROMATIN REMODELING 35
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsWongpalee SP / Liu S
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM130272 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)R01GM071940 United States
CitationJournal: Nat Commun / Year: 2019
Title: CryoEM structures of Arabidopsis DDR complexes involved in RNA-directed DNA methylation.
Authors: Somsakul Pop Wongpalee / Shiheng Liu / Javier Gallego-Bartolomé / Alexander Leitner / Ruedi Aebersold / Wanlu Liu / Linda Yen / Maria A Nohales / Peggy Hsuanyu Kuo / Ajay A Vashisht / James ...Authors: Somsakul Pop Wongpalee / Shiheng Liu / Javier Gallego-Bartolomé / Alexander Leitner / Ruedi Aebersold / Wanlu Liu / Linda Yen / Maria A Nohales / Peggy Hsuanyu Kuo / Ajay A Vashisht / James A Wohlschlegel / Suhua Feng / Steve A Kay / Z Hong Zhou / Steven E Jacobsen /
Abstract: Transcription by RNA polymerase V (Pol V) in plants is required for RNA-directed DNA methylation, leading to transcriptional gene silencing. Global chromatin association of Pol V requires components ...Transcription by RNA polymerase V (Pol V) in plants is required for RNA-directed DNA methylation, leading to transcriptional gene silencing. Global chromatin association of Pol V requires components of the DDR complex DRD1, DMS3 and RDM1, but the assembly process of this complex and the underlying mechanism for Pol V recruitment remain unknown. Here we show that all DDR complex components co-localize with Pol V, and we report the cryoEM structures of two complexes associated with Pol V recruitment-DR (DMS3-RDM1) and DDR' (DMS3-RDM1-DRD1 peptide), at 3.6 Å and 3.5 Å resolution, respectively. RDM1 dimerization at the center frames the assembly of the entire complex and mediates interactions between DMS3 and DRD1 with a stoichiometry of 1 DRD1:4 DMS3:2 RDM1. DRD1 binding to the DR complex induces a drastic movement of a DMS3 coiled-coil helix bundle. We hypothesize that both complexes are functional intermediates that mediate Pol V recruitment.
History
DepositionApr 9, 2019-
Header (metadata) releaseApr 17, 2019-
Map releaseJul 24, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6oit
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20081.png

Downloads & links

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Map

FileDownload / File: emd_20081.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 240 pix.
= 256.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055 / Movie #1: 0.055
Minimum - Maximum-0.19972427 - 0.31865928
Average (Standard dev.)0.000008659987 (±0.006694993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 256.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z256.800256.800256.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.2000.3190.000

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Supplemental data

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Sample components

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Entire : DDR' complex of DRD1 peptide with DMS3 and RDM1

EntireName: DDR' complex of DRD1 peptide with DMS3 and RDM1
Components
  • Complex: DDR' complex of DRD1 peptide with DMS3 and RDM1
    • Protein or peptide: Protein RDM1
    • Protein or peptide: Protein DEFECTIVE IN MERISTEM SILENCING 3
    • Protein or peptide: Protein CHROMATIN REMODELING 35

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Supramolecule #1: DDR' complex of DRD1 peptide with DMS3 and RDM1

SupramoleculeName: DDR' complex of DRD1 peptide with DMS3 and RDM1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Protein RDM1

MacromoleculeName: Protein RDM1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 20.072426 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGSSHHHHHH SQDPSSMTME LRPSGDSGSS DVDAEISDGF SPLDTSHRDV ADEGSLLRRA EMYQDYMKQV PIPTNRGSLI PFTSWVGLS ISMKQLYGQP LHYLTNVLLQ RWDQSRFGTD SEEQRLDSII HPTKAEATIW LVEEIHRLTP SHLHMALLWR S DPMYHSFI DPIFPEK

UniProtKB: Protein RDM1

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Macromolecule #2: Protein DEFECTIVE IN MERISTEM SILENCING 3

MacromoleculeName: Protein DEFECTIVE IN MERISTEM SILENCING 3 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 49.821352 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MADLYPTGQQ ISFQTTPLNV QDPTRMMNLD QSSPVARNET QNGGGIAHAE FAMFNSKRLE SDLEAMGNKI KQHEDNLKFL KSQKNKMDE AIVDLQVHMS KLNSSPTPRS ENSDNSLQGE DINAQILRHE NSAAGVLSLV ETLHGAQASQ LMLTKGVVGV V AKLGKVND ...String:
MADLYPTGQQ ISFQTTPLNV QDPTRMMNLD QSSPVARNET QNGGGIAHAE FAMFNSKRLE SDLEAMGNKI KQHEDNLKFL KSQKNKMDE AIVDLQVHMS KLNSSPTPRS ENSDNSLQGE DINAQILRHE NSAAGVLSLV ETLHGAQASQ LMLTKGVVGV V AKLGKVND ENLSQILSNY LGTRSMLAVV CRNYESVTAL EAYDNHGNID INAGLHCLGS SIGREIGDSF DAICLENLRP YV GQHIADD LQRRLDLLKP KLPNGECPPG FLGFAVNMIQ IDPAYLLCVT SYGYGLRETL FYNLFSRLQV YKTRADMISA LPC ISDGAV SLDGGIIRKT GIFNLGNRDE VNVRFAKPTA SRTMDNYSEA EKKMKELKWK KEKTLEDIKR EQVLREHAVF NFGK KKEEF VRCLAQSSCT NQPMNTPRGT LESGKETAAA KFERQHMDSS TSAA

UniProtKB: Protein DEFECTIVE IN MERISTEM SILENCING 3

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Macromolecule #3: Protein CHROMATIN REMODELING 35

MacromoleculeName: Protein CHROMATIN REMODELING 35 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 7.915782 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GEFFAVSNML EALDSGKFGS VSKELEEIAD MRMDLVKRSI WLYPSLAYTV FEAEKTMDGG GGSDYKDDDD K

UniProtKB: Protein CHROMATIN REMODELING 35

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 47.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 620248
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1)

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